miga-base 0.2.0.9 → 0.2.1.0

metadata

@@ -1,83 +1,83 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.2.0.9
+  version: 0.2.1.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-04-13 00:00:00.000000000 Z
+date: 2016-04-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.7'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.7'
 - !ruby/object:Gem::Dependency
   name: daemons
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.2'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.2'
 - !ruby/object:Gem::Dependency
   name: json
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.8'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.8'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '11'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '11'
 - !ruby/object:Gem::Dependency
   name: test-unit
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '3'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '3'
 description: Microbial Genomes Atlas
@@ -88,9 +88,30 @@ extensions: []
 extra_rdoc_files:
 - README.md
 files:
+- Gemfile
+- LICENSE
+- README.md
+- Rakefile
+- actions/add_result.rb
+- actions/add_taxonomy.rb
+- actions/create_dataset.rb
+- actions/create_project.rb
+- actions/daemon.rb
+- actions/date.rb
+- actions/download_dataset.rb
+- actions/find_datasets.rb
+- actions/import_datasets.rb
+- actions/index_taxonomy.rb
+- actions/list_datasets.rb
+- actions/list_files.rb
+- actions/project_info.rb
+- actions/unlink_dataset.rb
+- bin/miga
+- lib/miga.rb
 - lib/miga/common.rb
 - lib/miga/daemon.rb
 - lib/miga/dataset.rb
+- lib/miga/dataset_result.rb
 - lib/miga/metadata.rb
 - lib/miga/project.rb
 - lib/miga/remote_dataset.rb
@@ -98,16 +119,7 @@ files:
 - lib/miga/tax_index.rb
 - lib/miga/taxonomy.rb
 - lib/miga/version.rb
-- lib/miga.rb
-- test/common_test.rb
-- test/daemon_test.rb
-- test/dataset_test.rb
-- test/metadata_test.rb
-- test/project_test.rb
-- test/remote_dataset_test.rb
-- test/tax_index_test.rb
-- test/taxonomy_test.rb
-- test/test_helper.rb
+- scripts/_distances_functions.bash
 - scripts/_distances_noref_nomulti.bash
 - scripts/_distances_ref_nomulti.bash
 - scripts/aai_distances.bash
@@ -128,29 +140,21 @@ files:
 - scripts/subclades.bash
 - scripts/trimmed_fasta.bash
 - scripts/trimmed_reads.bash
+- test/common_test.rb
+- test/daemon_test.rb
+- test/dataset_test.rb
+- test/metadata_test.rb
+- test/project_test.rb
+- test/remote_dataset_test.rb
+- test/tax_index_test.rb
+- test/taxonomy_test.rb
+- test/test_helper.rb
 - utils/adapters.fa
 - utils/mytaxa_scan.R
 - utils/mytaxa_scan.rb
 - utils/requirements.txt
 - utils/subclades-compile.rb
 - utils/subclades.R
-- bin/miga
-- actions/add_result
-- actions/add_taxonomy
-- actions/create_dataset
-- actions/create_project
-- actions/daemon
-- actions/download_dataset
-- actions/find_datasets
-- actions/import_datasets
-- actions/index_taxonomy
-- actions/list_datasets
-- actions/list_files
-- actions/unlink_dataset
-- Gemfile
-- Rakefile
-- README.md
-- LICENSE
 homepage: http://enve-omics.ce.gatech.edu/miga
 licenses:
 - Artistic-2.0
@@ -159,25 +163,25 @@ post_install_message:
 rdoc_options:
 - lib
 - README.md
-- --main
+- "--main"
 - README.md
-- --title
+- "--title"
 - MiGA
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '1.9'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.14
+rubygems_version: 2.5.1
 signing_key: 
 specification_version: 4
 summary: MiGA

data/actions/add_result

@@ -1,58 +0,0 @@
-#!/usr/bin/env ruby
-
-# @package MiGA
-# @license Artistic-2.0
-
-o = {q:true}
-opts = OptionParser.new do |opt|
-   opt.banner = <<BAN
-Registers a result.
-
-Usage: #{$0} #{File.basename(__FILE__)} [options]
-BAN
-   opt.separator ""
-   opt.on("-P", "--project PATH",
-      "(Mandatory) Path to the project to use."){ |v| o[:project]=v }
-   opt.on("-D", "--dataset PATH",
-      "(Mandatory if the result is dataset-specific) ID of the dataset to use."
-      ){ |v| o[:dataset]=v }
-   opt.on("-r", "--result STRING",
-      "(Mandatory) Name of the result to add.",
-      "Recognized names for dataset-specific results include:",
-      *MiGA::Dataset.RESULT_DIRS.keys.map{|n| " ~ #{n}"},
-      "Recognized names for project-wide results include:",
-      *MiGA::Project.RESULT_DIRS.keys.map{|n| " ~ #{n}"}){ |v| o[:name]=v }
-   opt.on("-v", "--verbose",
-      "Print additional information to STDERR."){ o[:q]=false }
-   opt.on("-d", "--debug INT", "Print debugging information to STDERR.") do |v|
-      v.to_i>1 ? MiGA::MiGA.DEBUG_TRACE_ON : MiGA::MiGA.DEBUG_ON
-   end
-   opt.on("-h", "--help", "Display this screen.") do
-      puts opt
-      exit
-   end
-   opt.separator ""
-end.parse!
-
-
-### MAIN
-opts.parse!
-raise "-P is mandatory." if o[:project].nil?
-raise "-r is mandatory." if o[:name].nil?
-
-$stderr.puts "Loading project." unless o[:q]
-p = MiGA::Project.load(o[:project])
-raise "Impossible to load project: #{o[:project]}" if p.nil?
-
-$stderr.puts "Registering result." unless o[:q]
-if o[:dataset].nil?
-   r = p.add_result o[:name].to_sym
-else
-   d = p.dataset(o[:dataset])
-   r = d.add_result o[:name].to_sym
-end
-
-raise "Cannot add result, incomplete expected files." if r.nil?
-
-$stderr.puts "Done." unless o[:q]
-

data/actions/add_taxonomy

@@ -1,83 +0,0 @@
-#!/usr/bin/env ruby
-
-# @package MiGA
-# @license Artistic-2.0
-
-o = {q:true}
-OptionParser.new do |opt|
-   opt.banner = <<BAN
-Registers taxonomic information for datasets.
-
-Usage: #{$0} #{File.basename(__FILE__)} [options]
-BAN
-   opt.separator ""
-   opt.on("-P", "--project PATH",
-      "(Mandatory) Path to the project to use."){ |v| o[:project]=v }
-   opt.on("-D", "--dataset PATH",
-      "(Mandatory unless -t is provided) ID of the dataset to use."
-      ){ |v| o[:dataset]=v }
-   opt.on("-s", "--tax-string STRING",
-      "(Mandatory unless -t is provided) String corresponding to the taxonomy",
-      "of the dataset. The MiGA format of string taxonomy is a space-delimited",
-      "set of 'rank:name' pairs."){ |v| o[:taxstring]=v }
-   opt.on("-t", "--tax-file PATH",
-      "(Mandatory unless -D and -s are provided) Tab-delimited file containing",
-      "datasets taxonomy.  Each row corresponds to a datasets and each column",
-      "corresponds to a rank.  The first row must be a header with the rank ",
-      "names, and the first column must contain dataset names."
-      ){ |v| o[:taxfile]=v }
-   opt.on("-v", "--verbose",
-      "Print additional information to STDERR."){ o[:q]=false }
-   opt.on("-d", "--debug INT", "Print debugging information to STDERR.") do |v|
-      v.to_i>1 ? MiGA::MiGA.DEBUG_TRACE_ON : MiGA::MiGA.DEBUG_ON
-   end
-   opt.on("-h", "--help", "Display this screen.") do
-      puts opt
-      exit
-   end
-   opt.separator ""
-end.parse!
-
-
-### MAIN
-raise "-P is mandatory." if o[:project].nil?
-raise "-D is mandatory unless -t is provided." if
-   o[:dataset].nil? and o[:taxfile].nil?
-raise "-s is mandatory unless -t is provided." if
-   o[:taxstring].nil? and o[:taxfile].nil?
-
-$stderr.puts "Loading project." unless o[:q]
-p = MiGA::Project.load(o[:project])
-raise "Impossible to load project: #{o[:project]}" if p.nil?
-
-if not o[:taxfile].nil?
-   $stderr.puts "Reading tax-file and registering taxonomy." unless o[:q]
-   tfh = File.open(o[:taxfile], "r")
-   header = nil
-   tfh.each_line do |ln|
-      next if ln =~ /^\s*?$/
-      r = ln.chomp.split(/\t/, -1)
-      dn = r.shift
-      if header.nil?
-	 header = r
-	 next
-      end
-      d = p.dataset dn
-      if d.nil?
-	 warn "Impossible to find dataset at line #{$.}: #{dn}. Ignoring..."
-	 next
-      end
-      d.metadata[:tax] = MiGA::Taxonomy.new(r, header)
-      d.save
-      $stderr.puts " #{d.name} registered." unless o[:q]
-   end
-   tfh.close
-else
-   $stderr.puts "Registering taxonomy." unless o[:q]
-   d = p.dataset o[:dataset]
-   d.metadata[:tax] = MiGA::Taxonomy.new(o[:taxstring])
-   d.save
-end
-
-$stderr.puts "Done." unless o[:q]
-

data/actions/create_dataset

@@ -1,61 +0,0 @@
-#!/usr/bin/env ruby
-
-# @package MiGA
-# @license Artistic-2.0
-
-o = {q:true, ref:true}
-OptionParser.new do |opt|
-   opt.banner = <<BAN
-Creates an empty dataset in a pre-existing MiGA project.
-
-Usage: #{$0} #{File.basename(__FILE__)} [options]
-BAN
-   opt.separator ""
-   opt.on("-P", "--project PATH",
-      "(Mandatory) Path to the project to use."){ |v| o[:project]=v }
-   opt.on("-D", "--dataset STRING",
-      "(Mandatory) ID of the dataset to create."){ |v| o[:dataset]=v }
-   opt.on("-t", "--type STRING",
-      "Type of dataset. Recognized types include:",
-      *MiGA::Dataset.KNOWN_TYPES.map{ |k,v| "~ #{k}: #{v[:description]}"}
-      ){ |v| o[:type]=v.to_sym }
-   opt.on("-q", "--query",
-      "If set, the dataset is registered as a query, not a reference dataset."
-      ){ |v| o[:ref]=!v }
-   opt.on("-d", "--description STRING",
-      "Description of the dataset."){ |v| o[:description]=v }
-   opt.on("-u", "--user STRING",
-      "Owner of the dataset."){ |v| o[:user]=v }
-   opt.on("-c", "--comments STRING",
-      "Comments on the dataset."){ |v| o[:comments]=v }
-   opt.on("-v", "--verbose", 
-      "Print additional information to STDERR."){ o[:q]=false }
-   opt.on("-d", "--debug INT", "Print debugging information to STDERR.") do |v|
-      v.to_i>1 ? MiGA::MiGA.DEBUG_TRACE_ON : MiGA::MiGA.DEBUG_ON
-   end
-   opt.on("-h", "--help", "Display this screen.") do
-      puts opt
-      exit
-   end
-   opt.separator ""
-end.parse!
-
-
-### MAIN
-raise "-P is mandatory." if o[:project].nil?
-raise "-D is mandatory." if o[:dataset].nil?
-
-$stderr.puts "Loading project." unless o[:q]
-p = MiGA::Project.load(o[:project])
-raise "Impossible to load project: #{o[:project]}" if p.nil?
-
-$stderr.puts "Creating dataset." unless o[:q]
-md = {}
-[:type, :description, :user, :comments].each{ |k| md[k]=o[k] unless o[k].nil? }
-MiGA::Dataset.new(p, o[:dataset], o[:ref], md)
-p.add_dataset(o[:dataset])
-res = d.first_preprocessing
-put "- #{res}" unless o[:q]
-
-$stderr.puts "Done." unless o[:q]
-

data/actions/create_project

@@ -1,67 +0,0 @@
-#!/usr/bin/env ruby
-
-# @package MiGA
-# @license Artistic-2.0
-
-o = {q:true, update:false}
-OptionParser.new do |opt|
-   opt.banner = <<BAN
-Creates an empty MiGA project.
-
-Usage: #{$0} #{File.basename(__FILE__)} [options]
-BAN
-   opt.separator ""
-   opt.on("-P", "--project PATH",
-      "(Mandatory) Path to the project to create."){ |v| o[:project]=v }
-   opt.on("-t", "--type STRING",
-      "Type of dataset. Recognized types include:", 
-      *MiGA::Project.KNOWN_TYPES.map{ |k,v| "~ #{k}: #{v[:description]}"}
-      ){ |v| o[:type]=v.to_sym }
-   opt.on("-n", "--name STRING",
-      "Name of the project."){ |v| o[:name]=v }
-   opt.on("-d", "--description STRING",
-      "Description of the project."){ |v| o[:description]=v }
-   opt.on("-u", "--user STRING", "Owner of the project."){ |v| o[:user]=v }
-   opt.on("-c", "--comments STRING",
-      "Comments on the project."){ |v| o[:comments]=v }
-   opt.on("--update",
-      "Updates the project if it already exists."){ o[:update]=true }
-   opt.on("-v", "--verbose",
-      "Print additional information to STDERR."){ o[:q]=false }
-   opt.on("-d", "--debug INT", "Print debugging information to STDERR.") do |v|
-      v.to_i>1 ? MiGA::MiGA.DEBUG_TRACE_ON : MiGA::MiGA.DEBUG_ON
-   end
-   opt.on("-h", "--help", "Display this screen.") do
-      puts opt
-      exit
-   end
-   opt.separator ""
-end.parse!
-
-
-### MAIN
-raise "-P is mandatory." if o[:project].nil?
-
-unless File.exist? "#{ENV["HOME"]}/.miga_rc" and
-      File.exist? "#{ENV["HOME"]}/.miga_daemon.json"
-   puts "You must initialize MiGA before creating the first project.\n" +
-      "Do you want to initialize MiGA now? (yes / no)"
-   `'#{File.dirname(__FILE__)}/../scripts/init.bash'` if
-      $stdin.gets.chomp == 'yes'
-end
-
-$stderr.puts "Creating project." unless o[:q]
-raise "Project already exists, aborting." unless
-   o[:update] or not MiGA::Project.exist? o[:project]
-p = MiGA::Project.new(o[:project], o[:update])
-# The following check is redundant with MiGA::Project#create,
-# but allows upgrading projects from (very) early code versions
-o[:name] = File.basename(p.path) if
-   o[:update] and o[:name].nil?
-[:name, :description, :user, :comments, :type].each do |k|
-   p.metadata[k] = o[k] unless o[k].nil?
-end
-p.save
-
-$stderr.puts "Done." unless o[:q]
-